The Modular Organization of Protein Interactions in Escherichia coli.
Escherichia coli serves as an excellent model for the study of fundamental cellular processes such as metabolism, signalling and gene expression. Understanding the function and organization of proteins within these processes is an important step towards a 'systems' view of E. coli. Integra...
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| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2009-10-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1000523 |
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| _version_ | 1850163047994228736 |
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| author | José M Peregrín-Alvarez Xuejian Xiong Chong Su John Parkinson |
| author_facet | José M Peregrín-Alvarez Xuejian Xiong Chong Su John Parkinson |
| author_sort | José M Peregrín-Alvarez |
| collection | DOAJ |
| description | Escherichia coli serves as an excellent model for the study of fundamental cellular processes such as metabolism, signalling and gene expression. Understanding the function and organization of proteins within these processes is an important step towards a 'systems' view of E. coli. Integrating experimental and computational interaction data, we present a reliable network of 3,989 functional interactions between 1,941 E. coli proteins ( approximately 45% of its proteome). These were combined with a recently generated set of 3,888 high-quality physical interactions between 918 proteins and clustered to reveal 316 discrete modules. In addition to known protein complexes (e.g., RNA and DNA polymerases), we identified modules that represent biochemical pathways (e.g., nitrate regulation and cell wall biosynthesis) as well as batteries of functionally and evolutionarily related processes. To aid the interpretation of modular relationships, several case examples are presented, including both well characterized and novel biochemical systems. Together these data provide a global view of the modular organization of the E. coli proteome and yield unique insights into structural and evolutionary relationships in bacterial networks. |
| format | Article |
| id | doaj-art-d0a5e25c3bd14798bf2065ee7ea09b18 |
| institution | OA Journals |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2009-10-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-d0a5e25c3bd14798bf2065ee7ea09b182025-08-20T02:22:24ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582009-10-01510e100052310.1371/journal.pcbi.1000523The Modular Organization of Protein Interactions in Escherichia coli.José M Peregrín-AlvarezXuejian XiongChong SuJohn ParkinsonEscherichia coli serves as an excellent model for the study of fundamental cellular processes such as metabolism, signalling and gene expression. Understanding the function and organization of proteins within these processes is an important step towards a 'systems' view of E. coli. Integrating experimental and computational interaction data, we present a reliable network of 3,989 functional interactions between 1,941 E. coli proteins ( approximately 45% of its proteome). These were combined with a recently generated set of 3,888 high-quality physical interactions between 918 proteins and clustered to reveal 316 discrete modules. In addition to known protein complexes (e.g., RNA and DNA polymerases), we identified modules that represent biochemical pathways (e.g., nitrate regulation and cell wall biosynthesis) as well as batteries of functionally and evolutionarily related processes. To aid the interpretation of modular relationships, several case examples are presented, including both well characterized and novel biochemical systems. Together these data provide a global view of the modular organization of the E. coli proteome and yield unique insights into structural and evolutionary relationships in bacterial networks.https://doi.org/10.1371/journal.pcbi.1000523 |
| spellingShingle | José M Peregrín-Alvarez Xuejian Xiong Chong Su John Parkinson The Modular Organization of Protein Interactions in Escherichia coli. PLoS Computational Biology |
| title | The Modular Organization of Protein Interactions in Escherichia coli. |
| title_full | The Modular Organization of Protein Interactions in Escherichia coli. |
| title_fullStr | The Modular Organization of Protein Interactions in Escherichia coli. |
| title_full_unstemmed | The Modular Organization of Protein Interactions in Escherichia coli. |
| title_short | The Modular Organization of Protein Interactions in Escherichia coli. |
| title_sort | modular organization of protein interactions in escherichia coli |
| url | https://doi.org/10.1371/journal.pcbi.1000523 |
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